Ultraspecific probes for high throughput HLA typing.
Ultraspecific probes for high throughput HLA typing.
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DOI：
10.1186/1471-2164-10-85
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发表时间：
2009-02-20
期刊：
影响因子：
4.4
通讯作者：
Fofanov Y
中科院分区：
文献类型：
--
作者：
Feng C;Putonti C;Zhang M;Eggers R;Mitra R;Hogan M;Jayaraman K;Fofanov Y
人类白细胞抗原(人类白细胞抗原)基因的变异与许多免疫学事件有关，如疾病易感性、对疫苗的反应以及血液、组织和器官移植的成功。尽管微阵列格式具有实现高分辨率分型的潜力，但由于当前探针设计策略的低效，这一点尚未实现。我们提出了一种新的三步法来设计高通量的人类白细胞抗原分型微阵列分析方法。该方法首先选择包含存在于感兴趣基因的所有等位基因中的SNP的序列，然后计算将候选探测序列转换为可能存在于包括人类基因组其余部分的样本中的序列集中最接近的子序列所需的碱基改变的数目，以便识别那些对感兴趣的等位基因具有超特异性的候选探针。由于这些序列的高度特异性，有可能不再需要像PCR扩增这样的初步步骤。最后，选择这些超特异探针的最小数量，以便可以在最小的生产成本下实现最高分辨率的分型。作为一个例子，设计了一个阵列，并在电子计算机中获得了用于人类白细胞抗原-B位点分型的结果。这里介绍的分析提供了比以前开发的更高的分辨率，并且包括比以前认为的更多的等位基因。基于计算机实验和初步的实验结果，我们相信所提出的方法可以很容易地应用于任何高度多态的基因系统。
The variations within an individual's HLA (Human Leukocyte Antigen) genes have been linked to many immunological events, e.g. susceptibility to disease, response to vaccines, and the success of blood, tissue, and organ transplants. Although the microarray format has the potential to achieve high-resolution typing, this has yet to be attained due to inefficiencies of current probe design strategies. We present a novel three-step approach for the design of high-throughput microarray assays for HLA typing. This approach first selects sequences containing the SNPs present in all alleles of the locus of interest and next calculates the number of base changes necessary to convert a candidate probe sequences to the closest subsequence within the set of sequences that are likely to be present in the sample including the remainder of the human genome in order to identify those candidate probes which are "ultraspecific" for the allele of interest. Due to the high specificity of these sequences, it is possible that preliminary steps such as PCR amplification are no longer necessary. Lastly, the minimum number of these ultraspecific probes is selected such that the highest resolution typing can be achieved for the minimal cost of production. As an example, an array was designed and in silico results were obtained for typing of the HLA-B locus. The assay presented here provides a higher resolution than has previously been developed and includes more alleles than previously considered. Based upon the in silico and preliminary experimental results, we believe that the proposed approach can be readily applied to any highly polymorphic gene system.
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影响因子：
4.1
作者：
Ye, BC;Chu, XH;Zuo, P
通讯作者：
Zuo, P
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NEPOM, GT;BYERS, P;NEPOM, BS
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2.6
作者：
Listì, F;Candore, G;Caruso, C
通讯作者：
Caruso, C